fix lint checks

scripts/lint.sh

@@ -6,4 +6,4 @@ if [ -n "$noflow" ]; then
   exit 1
 fi
 
-./node_modules/.bin/jsxhint --es6module --harmony 'main/src/**/*.js' 'main/test/**/*.js'
+./node_modules/.bin/jsxhint --es6module --harmony 'src/main/**/*.js' 'src/test/**/*.js'

src/main/DisplayMode.js

@@ -3,6 +3,7 @@
  * This enum & associated functions help track these transitions.
  * @flow
  */
+'use strict';
 
 var DisplayMode = {
   LOOSE: 1,   // Lots of space -- a big font is OK.

src/main/GA4GHAlignment.js

@@ -3,6 +3,7 @@
  * pileup.js Alignment type.
  * @flow
  */
+'use strict';
 
 import type {CigarOp, MateProperties, Strand} from './Alignment';
 
@@ -91,6 +92,6 @@ class GA4GHAlignment /* implements Alignment */ {
     // this.alignment.id would be appealing here, but it's not actually unique!
     return alignment.fragmentName + ':' + alignment.readNumber;
   }
-};
+}
 
 module.exports = GA4GHAlignment;

src/main/GA4GHDataSource.js

@@ -3,6 +3,7 @@
  * Currently only used to load alignments.
  * @flow
  */
+'use strict';
 
 import type {Alignment, AlignmentDataSource} from './Alignment';
 

src/main/LocationTrack.js

@@ -81,7 +81,7 @@ class LocationTrack extends React.Component {
 LocationTrack.propTypes = {
   range: types.GenomeRange.isRequired,
 };
-LocationTrack.displayName = 'location'
+LocationTrack.displayName = 'location';
 LocationTrack.defaultSource = EmptySource.create();
 
 module.exports = LocationTrack;

src/main/PileupCache.js

@@ -87,27 +87,26 @@ class PileupCache {
     };
     group.alignments.push(visualAlignment);
 
+    var mateInterval = null;
     if (group.alignments.length == 1) {
       // This is the first read in the group. Infer its span from its mate properties.
       // TODO: if the mate Alignment is also available, it would be better to use that.
       var intervals = [range];
       var mateProps = read.getMateProperties();
       if (mateProps && mateProps.ref && mateProps.ref == read.ref) {
-        var mateInterval = new ContigInterval(mateProps.ref, mateProps.pos, mateProps.pos + range.length());
+        mateInterval = new ContigInterval(mateProps.ref, mateProps.pos, mateProps.pos + range.length());
         intervals.push(mateInterval);
       }
-      var {span, insert} = spanAndInsert(intervals);
-      group.insert = insert;
-      group.span = span;
+      group = _.extend(group, spanAndInsert(intervals));
 
       if (!(read.ref in this.refToPileup)) {
         this.refToPileup[read.ref] = [];
       }
       var pileup = this.refToPileup[read.ref];
-      group.row = addToPileup(span.interval, pileup);
+      group.row = addToPileup(group.span.interval, pileup);
     } else if (group.alignments.length == 2) {
       // Refine the connector
-      var mateInterval = group.alignments[0].read.getInterval();
+      mateInterval = group.alignments[0].read.getInterval();
       var {span, insert} = spanAndInsert([range, mateInterval]);
       group.insert = insert;
       if (insert) {

src/main/PileupTrack.js

@@ -90,10 +90,10 @@ function getRenderer(ctx: DataCanvasRenderingContext2D, scale: (num: number) =>
       case CigarOp.INSERT:
         ctx.save();
         ctx.fillStyle = style.INSERT_COLOR;
-        var x = scale(op.pos + 1) - 2,  // to cover a bit of the previous segment
+        var x0 = scale(op.pos + 1) - 2,  // to cover a bit of the previous segment
             y1 = y - 1,
             y2 = y + READ_HEIGHT + 2;
-        ctx.fillRect(x, y1, 1, y2 - y1);
+        ctx.fillRect(x0, y1, 1, y2 - y1);
         ctx.restore();
         break;
     }
@@ -138,7 +138,7 @@ function getRenderer(ctx: DataCanvasRenderingContext2D, scale: (num: number) =>
     ctx.popObject();
   }
 
-  return {drawArrow, drawSegment, drawGroup}
+  return {drawArrow, drawSegment, drawGroup};
 }
 
 
@@ -293,6 +293,7 @@ class PileupTrack extends React.Component {
     var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y);
     this.renderScene(trackingCtx);
     var vRead = trackingCtx.hit && trackingCtx.hit[0];
+    var alert = window.alert || console.log;
     if (vRead) {
       alert(vRead.read.debugString());
     }

src/main/SamRead.js

@@ -18,7 +18,6 @@ import type {Strand, CigarOp, MateProperties} from './Alignment';
 var jDataView = require('jdataview'),
     jBinary = require('jbinary'),
     _ = require('underscore'),
-    {nullString} = require('./formats/helpers'),
     bamTypes = require('./formats/bamTypes'),
     ContigInterval = require('./ContigInterval');
 

src/main/VariantTrack.js

@@ -94,6 +94,7 @@ var VariantTrack = React.createClass({
     var trackingCtx = new dataCanvas.ClickTrackingContext(ctx, x, y);
     this.renderScene(trackingCtx);
     var variant = trackingCtx.hit && trackingCtx.hit[0];
+    var alert = window.alert || console.log;
     if (variant) {
       alert(JSON.stringify(variant));
     }

src/main/VisualizationWrapper.js

@@ -1,6 +1,7 @@
 /**
  * @flow
  */
+'use strict';
 
 var React = require('./react-shim'),
     types = require('./react-types'),

src/main/canvas-utils.js

@@ -3,6 +3,7 @@
  *
  * @flow
  */
+'use strict';
 
 // Return the 2D context for a canvas. This is helpful for type safety.
 function getContext(el: Element): CanvasRenderingContext2D {
@@ -23,4 +24,4 @@ function drawLine(ctx: CanvasRenderingContext2D, x1: number, y1: number, x2: num
 module.exports = {
   getContext,
   drawLine
-}
+};

src/main/d3utils.js

@@ -43,7 +43,7 @@ function sizeCanvas(el: HTMLCanvasElement, width: number, height: number) {
   el.style.width = width + 'px';
   el.style.height = height + 'px';
   var ctx = el.getContext('2d');
-  if (ctx != null && ctx instanceof CanvasRenderingContext2D) {
+  if (ctx !== null && ctx instanceof CanvasRenderingContext2D) {
     ctx.scale(ratio, ratio);
   }
 }

src/main/pileup.js

@@ -79,13 +79,13 @@ function create(elOrId: string|Element, params: PileupParams): Pileup {
                          initialRange={params.range} />, el);
   return {
     setRange(range: GenomeRange) {
-      if (reactElement == null) {
+      if (reactElement === null) {
         throw 'Cannot call setRange on a destroyed pileup';
       }
       reactElement.handleRangeChange(range);
     },
     getRange(): GenomeRange {
-      if (reactElement == null) {
+      if (reactElement === null) {
         throw 'Cannot call setRange on a destroyed pileup';
       }
       return _.clone(reactElement.state.range);

src/test/CoverageTrack-test.js

@@ -8,19 +8,12 @@
 
 var expect = require('chai').expect;
 
-var Q = require('q'),
-    _ = require('underscore');
-
 import type * as SamRead from '../main/SamRead';
 
 var pileup = require('../main/pileup'),
     TwoBit = require('../main/TwoBit'),
     TwoBitDataSource = require('../main/TwoBitDataSource'),
-    Bam = require('../main/bam'),
-    BamDataSource = require('../main/BamDataSource'),
-    RemoteFile = require('../main/RemoteFile'),
     MappedRemoteFile = require('./MappedRemoteFile'),
-    ContigInterval = require('../main/ContigInterval'),
     dataCanvas = require('data-canvas'),
     {waitFor} = require('./async');
 
@@ -73,7 +66,7 @@ describe('CoverageTrack', function() {
   };
 
   var findCoverageLabels = () => {
-    return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label')
+    return drawnObjectsWith(testDiv, '.coverage', l => l.type == 'label');
   };
 
   var hasCoverage = () => {

src/test/GA4GHAlignment-test.js

@@ -1,10 +1,10 @@
 /** @flow */
+'use strict';
 
 var expect = require('chai').expect;
 
 var GA4GHAlignment = require('../main/GA4GHAlignment'),
     RemoteFile = require('../main/RemoteFile'),
-    SamRead = require('../main/SamRead'),
     Bam = require('../main/bam');
 
 describe('GA4GHAlignment', function() {

src/test/GA4GHDataSource-test.js

@@ -1,15 +1,14 @@
 /** @flow */
+'use strict';
 
 var expect = require('chai').expect;
 
 var sinon = require('sinon');
 
 var ContigInterval = require('../main/ContigInterval'),
     GA4GHDataSource = require('../main/GA4GHDataSource'),
-    RemoteFile = require('../main/RemoteFile'),
-    SamRead = require('../main/SamRead'),
-    Bam = require('../main/bam');
-
+    RemoteFile = require('../main/RemoteFile');
+
 describe('GA4GHDataSource', function() {
   var server: any = null, response;
 

src/test/GeneTrack-test.js

@@ -9,14 +9,8 @@
 
 var expect = require('chai').expect;
 
-var React = require('../main/react-shim');
-var Q = require('q');
-
 var pileup = require('../main/pileup'),
-    TwoBit = require('../main/TwoBit'),
-    TwoBitDataSource = require('../main/TwoBitDataSource'),
     dataCanvas = require('data-canvas'),
-    MappedRemoteFile = require('./MappedRemoteFile'),
     {waitFor} = require('./async');
 
 describe('GeneTrack', function() {

src/test/PileupCache-test.js

@@ -9,8 +9,7 @@ var expect = require('chai').expect;
 var _ = require('underscore');
 
 var PileupCache = require('../main/PileupCache'),
-    ContigInterval = require('../main/ContigInterval'),
-    Interval = require('../main/Interval');
+    ContigInterval = require('../main/ContigInterval');
 
 var numAlignments = 1;
 class TestAlignment /* implements Alignment */ {
@@ -56,11 +55,6 @@ function makeReadPair(range1: ContigInterval<string>, range2: ContigInterval<str
   ];
 }
 
-function makeUnpairedRead(range: ContigInterval<string>, strand: Strand): Alignment {
-  var name = 'group:' + (nameCounter++);
-  return new TestAlignment(range, name, strand, null);
-}
-
 function dieFn() { throw 'Should not have called this.'; }
 var fakeSource = {
   rangeChanged: dieFn,
@@ -75,7 +69,9 @@ var fakeSource = {
 };
 
 describe('PileupCache', function() {
-  function ci(...x: any) { return new ContigInterval(...x); }
+  function ci(chr: string, start: number, end:number) {
+    return new ContigInterval(chr, start, end);
+  }
 
   function makeCache(args) {
     var cache = new PileupCache(fakeSource);

src/test/PileupTrack-test.js

@@ -128,7 +128,7 @@ describe('PileupTrack', function() {
     return {p, fakeTwoBit, fakeBam};
   }
 
-  var {drawnObjectsWith, callsOf} = dataCanvas.RecordingContext;
+  var {drawnObjectsWith} = dataCanvas.RecordingContext;
 
   var hasReference = () => {
       // The reference initially shows "unknown" base pairs, so we have to
@@ -150,7 +150,7 @@ describe('PileupTrack', function() {
       var ref = drawnObjectsWith(testDiv, '.reference', x => x.pos == 7500765 - 1);
       expect(ref).to.have.length(1);
       expect(ref[0].letter).to.equal('C');
-      
+
       var mismatches = mismatchesAtPos(7500765 - 1);
       expect(mismatches).to.have.length(22);
       _.each(mismatches, mm => {

src/test/components-test.js

@@ -5,9 +5,8 @@ var expect = require('chai').expect;
 
 var pileup = require('../main/pileup'),
     {waitFor} = require('./async'),
-    dataCanvas = require('data-canvas'),
-    _ = require('underscore');
-
+    dataCanvas = require('data-canvas');
+
 describe('pileup', function() {
   var tracks = [
     {

src/test/pileuputils-test.js

@@ -118,7 +118,7 @@ describe('pileuputils', function() {
     };
 
     var unknownReferenceSource = {
-      getRangeAsString: function({contig, start, stop}) {
+      getRangeAsString: function({start, stop}) {
         return _.range(start, stop + 1).map(x => '.').join('');
       }
     };